Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Seq::LargeLocatableSeq - LocatableSeq object that stores sequence as files in the


         # normal primary seq usage
           use Bio::Seq::LargeLocatableSeq;
           my $seq = Bio::Seq::LargeLocatableSeq->new(-seq => "CAGT-GGT",
                                                     -id  => "seq1",
                                                     -start => 1,
                                                     -end   => 7);


       Bio::Seq::LargeLocatableSeq - object with start/end points on it that can be projected
       into a MSA or have coordinates relative to another seq.

       This object, unlike Bio::LocatableSeq, stores a sequence as a series of files in a
       temporary directory. The aim is to allow someone the ability to store very large sequences
       (eg, > 100MBases) in a file system without running out of memory (eg, on a 64 MB real
       memory machine!).

       Of course, to actually make use of this functionality, the programs which use this object
       must not call $primary_seq->seq otherwise the entire sequence will come out into memory
       and probably crash your machine. However, calls like $primary_seq->subseq(10,100) will
       cause only 90 characters to be brought into real memory.


   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.
                  - General discussion  - About the mailing lists

       Please direct usage questions or support issues to the mailing list:

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

AUTHOR - Albert Vilella

       Email avilella-AT-gmail-DOT-com


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : my $obj = Bio::Seq::LargeLocatableSeq->new();
        Function: Builds a new Bio::Seq::LargeLocatableSeq object
        Returns : an instance of Bio::Seq::LargeLocatableSeq
        Args    :

        Title   : length
        Usage   :
        Example :
        Returns :
        Args    :

        Title   : seq
        Usage   :
        Example :
        Returns :
        Args    :

        Title   : subseq
        Usage   :
        Example :
        Returns :
        Args    :

        Title   : add_sequence_as_string
        Usage   : $seq->add_sequence_as_string("CATGAT");
        Function: Appends additional residues to an existing LargeLocatableSeq object.
                  This allows one to build up a large sequence without storing
                  entire object in memory.
        Returns : Current length of sequence
        Args    : string to append

        Title   : _filename
        Usage   : $obj->_filename($newval)
        Example :
        Returns : value of _filename
        Args    : newvalue (optional)

        Title   : alphabet
        Usage   : $obj->alphabet($newval)
        Example :
        Returns : value of alphabet
        Args    : newvalue (optional)